Bayesian inference of infectious disease transmission from whole-genome sequence data (Q30796685)

27 September 2017

Bayesian inference of infectious disease transmission from whole-genome sequence data (English)

1 reference

27 September 2017

1 reference

1 reference

whole genome sequencing

1 reference

1 reference

27 September 2017

Jennifer Gardy

0 references

Caroline Colijn

1 reference

27 September 2017

8 April 2014

1 reference

Molecular Biology and Evolution

27 September 2017

1 reference

27 September 2017

1 reference

27 September 2017

1 reference

27 September 2017

1869-1879

1 reference

PMC publication ID

4069612

describes a project that uses

27 September 2017

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Diverse sources of C. difficile infection identified on whole-genome sequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Relating phylogenetic trees to transmission trees of infectious disease outbreaks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Genomic evolution and transmission of Helicobacter pylori in two South African families.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Selected insights from application of whole-genome sequencing for outbreak investigations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

How the dynamics and structure of sexual contact networks shape pathogen phylogenies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Within-host evolution of Staphylococcus aureus during asymptomatic carriage.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Overview of molecular typing methods for outbreak detection and epidemiological surveillance.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

A Bayesian inference framework to reconstruct transmission trees using epidemiological and genetic data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Routine use of microbial whole genome sequencing in diagnostic and public health microbiology

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Transforming clinical microbiology with bacterial genome sequencing.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Role of donor genital tract HIV-1 diversity in the transmission bottleneck

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Estimating the basic reproductive number from viral sequence data.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Helicobacter pylori genome evolution during human infection

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Whole-genome sequencing and social-network analysis of a tuberculosis outbreak

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Cytoscape 2.8: new features for data integration and network visualization

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Epidemiological and clinical consequences of within-host evolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Reconstructing disease outbreaks from genetic data: a graph approach

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Evolutionary analysis of the dynamics of viral infectious disease

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

The Sequence Alignment/Map format and SAMtools

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Fast and accurate short read alignment with Burrows-Wheeler transform

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Transmission pathways of foot-and-mouth disease virus in the United Kingdom in 2007

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

BEAST: Bayesian evolutionary analysis by sampling trees

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Inference of bacterial microevolution using multilocus sequence data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Network biology: understanding the cell's functional organization

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Unifying the epidemiological and evolutionary dynamics of pathogens

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

A tutorial introduction to Bayesian inference for stochastic epidemic models using Markov chain Monte Carlo methods.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Duration of colonization by methicillin-resistant Staphylococcus aureus after hospital discharge and risk factors for prolonged carriage

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Criteria for the control of drug-resistant tuberculosis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Inferring coalescence times from DNA sequence data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

Sampling theory for neutral alleles in a varying environment.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069612

DensiTree: making sense of sets of phylogenetic trees

14 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU121

Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU121

Carriage of methicillin-resistant Staphylococcus aureus among hospital employees: prevalence, duration, and transmission to households.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU121

A general method for numerically simulating the stochastic time evolution of coupled chemical reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU121

Reversible jump Markov chain Monte Carlo computation and Bayesian model determination

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU121

Duration of methicillin-resistant Staphylococcus aureus carriage, according to risk factors for acquisition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU121

Accounting for phylogenetic uncertainty in biogeography: a Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: Turdus).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU121

Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU121

Genomic analysis to improve the management of outbreaks of bacterial infection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU121

21 January 2018

Identifiers

DOI

10.1093/MOLBEV/MSU121

1 reference

27 September 2017

1 reference

PMC publication ID

4069612

27 September 2017

PubMed publication ID

24714079

1 reference

PMC publication ID

4069612